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Add Atkin et al 2017 leaf respiration model #931

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merged 34 commits into from
Mar 7, 2023
Merged

Add Atkin et al 2017 leaf respiration model #931

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b907af7
starting to add hooks for multiple leaf maintenance respiration models
ckoven Nov 1, 2022
4e0d958
added Atkin et al 2017 respiration model
ckoven Nov 2, 2022
08d755c
bugfixes
ckoven Nov 3, 2022
bd091b0
fixed some Celsius vs Kelvin unit errors
ckoven Nov 3, 2022
5b372c9
changed vertical profile of leaf MR to be propotional to SLA and leaf…
ckoven Nov 15, 2022
a16e1b5
fixed bug in C4 respiration in prior version
ckoven Nov 15, 2022
1d90f6d
merged main and resolved conflicts
ckoven Dec 2, 2022
1f7d9af
merged main and resolved conflicts
ckoven Dec 2, 2022
8e582a6
merged two respiration branches
ckoven Dec 2, 2022
57572d3
added history diagnostic for running-mean Tgrowth variable
ckoven Jan 12, 2023
9fcdfa8
added history diagnostic for unreduced maintenance respiration
ckoven Jan 12, 2023
27d0c68
make Tgrowth and maintenance respiration reduction diagnostics inacti…
ckoven Jan 30, 2023
46fa764
reorganized C3/C4 logic to use separate subroutines
ckoven Jan 30, 2023
f5f1c9a
revert dark respiration model to the Ryan 1991 model
ckoven Jan 30, 2023
10db8b9
swapping hard-coded basal respiration rate in Ryan 1991 model with va…
ckoven Jan 30, 2023
27c5e78
removing PFT argument to Ryan 1991 respiration models as no longer ne…
ckoven Jan 31, 2023
22212b5
merged main and resolved conflicts
ckoven Feb 1, 2023
c2a1dd8
add xml patch file for update to api25.1.1
glemieux Feb 16, 2023
5c3fe60
fix missing third decimal place value in fates_base_mr_20
glemieux Feb 16, 2023
56b3266
Update xml file to old format to add new parameter value
glemieux Feb 22, 2023
10d686a
Update xml patch file for api25.1.1
glemieux Feb 23, 2023
8d680fa
Fix BatchPatchParams.py global history update call
glemieux Feb 24, 2023
c26f5c7
Use new Atkin parameter variable
glemieux Feb 24, 2023
6c00d7f
fix typo and comment out pft param registration
glemieux Feb 24, 2023
7e56708
Uncomment the atkin parameter registration and retrieval
glemieux Feb 27, 2023
8620f9e
Update maintenance respiration variable names
glemieux Feb 27, 2023
aa0375d
fix default param file name
glemieux Feb 28, 2023
59a865f
fix leaf model name assignment
glemieux Feb 28, 2023
5c97f6a
reverted C3/C4 logic to now use same model for all PFTs and same Atki…
ckoven Mar 1, 2023
fd9f5f6
Merge pull request #14 from glemieux/respiration-agnostic_vars
ckoven Mar 1, 2023
99ce45d
merged updates to parameter variable names and dimensions
ckoven Mar 1, 2023
ac8d58f
fixed bug from merge
ckoven Mar 1, 2023
a20b462
Rename the patch file api number
glemieux Mar 7, 2023
008f8f8
Minor instruction update in patch file
glemieux Mar 7, 2023
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3 changes: 3 additions & 0 deletions biogeochem/EDCohortDynamicsMod.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -611,6 +611,7 @@ subroutine nan_cohort(cc_p)
!RESPIRATION
currentCohort%rdark = nan
currentCohort%resp_m = nan ! Maintenance respiration. kGC/cohort/year
currentCohort%resp_m_unreduced = nan ! Diagnostic-only unreduced Maintenance respiration. kGC/cohort/year
currentCohort%resp_excess = nan ! Respiration of excess (unallocatable) carbon (kg/indiv/day)
currentCohort%livestem_mr = nan ! Live stem maintenance respiration. kgC/indiv/s-1
currentCohort%livecroot_mr = nan ! Coarse root maintenance respiration. kgC/indiv/s-1
Expand Down Expand Up @@ -668,6 +669,7 @@ subroutine zero_cohort(cc_p)
currentCohort%status_coh = 0
currentCohort%rdark = 0._r8
currentCohort%resp_m = 0._r8
currentCohort%resp_m_unreduced = 0._r8
currentCohort%resp_excess = 0._r8
currentCohort%resp_g_tstep = 0._r8
currentCohort%livestem_mr = 0._r8
Expand Down Expand Up @@ -1916,6 +1918,7 @@ subroutine copy_cohort( currentCohort,copyc )
!RESPIRATION
n%rdark = o%rdark
n%resp_m = o%resp_m
n%resp_m_unreduced= o%resp_m_unreduced
n%resp_excess = o%resp_excess
n%resp_g_tstep = o%resp_g_tstep
n%livestem_mr = o%livestem_mr
Expand Down
152 changes: 119 additions & 33 deletions biogeophys/FatesPlantRespPhotosynthMod.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -42,6 +42,9 @@ module FATESPlantRespPhotosynthMod
use PRTGenericMod, only : max_nleafage
use EDTypesMod, only : do_fates_salinity
use EDParamsMod, only : q10_mr
use EDParamsMod, only : maintresp_leaf_model
use FatesConstantsMod, only : lmrmodel_ryan_1991
use FatesConstantsMod, only : lmrmodel_atkin_etal_2017
use PRTGenericMod, only : prt_carbon_allom_hyp
use PRTGenericMod, only : prt_cnp_flex_allom_hyp
use PRTGenericMod, only : carbon12_element
Expand All @@ -52,7 +55,7 @@ module FATESPlantRespPhotosynthMod
use PRTGenericMod, only : store_organ
use PRTGenericMod, only : repro_organ
use PRTGenericMod, only : struct_organ
use EDParamsMod, only : ED_val_base_mr_20, stomatal_model, stomatal_assim_model
use EDParamsMod, only : maintresp_nonleaf_baserate, stomatal_model, stomatal_assim_model
use PRTParametersMod, only : prt_params
use EDPftvarcon , only : EDPftvarcon_inst

Expand Down Expand Up @@ -127,7 +130,6 @@ subroutine FatesPlantRespPhotosynthDrive (nsites, sites,bc_in,bc_out,dtime)
use FatesInterfaceTypesMod , only : bc_out_type
use EDCanopyStructureMod, only : calc_areaindex
use FatesConstantsMod, only : umolC_to_kgC
use FatesConstantsMod, only : g_per_kg
use FatesConstantsMod, only : umol_per_mmol
use FatesConstantsMod, only : rgas => rgas_J_K_kmol
use FatesParameterDerivedMod, only : param_derived
Expand Down Expand Up @@ -274,12 +276,6 @@ subroutine FatesPlantRespPhotosynthDrive (nsites, sites,bc_in,bc_out,dtime)
integer :: iage ! loop counter for leaf age classes

! Parameters
! -----------------------------------------------------------------------
! Base maintenance respiration rate for plant tissues base_mr_20
! M. Ryan, 1991. Effects of climate change on plant respiration.
! Ecological Applications, 1(2), 157-167.
! Original expression is br = 0.0106 molC/(molN h)
! Conversion by molecular weights of C and N gives 2.525e-6 gC/(gN s)
!
! Base rate is at 20C. Adjust to 25C using the CN Q10 = 1.5
! (gC/gN/s)
Expand Down Expand Up @@ -527,17 +523,33 @@ subroutine FatesPlantRespPhotosynthDrive (nsites, sites,bc_in,bc_out,dtime)

end select

! MLO - Shouldn't these numbers be parameters too?
lmr25top = 2.525e-6_r8 * (1.5_r8 ** ((25._r8 - 20._r8)/10._r8))
lmr25top = lmr25top * lnc_top / (umolC_to_kgC * g_per_kg)
! Part VII: Calculate dark respiration (leaf maintenance) for this layer

select case (maintresp_leaf_model)

! Part VII: Calculate dark respiration (leaf maintenance) for this layer
call LeafLayerMaintenanceRespiration( lmr25top, & ! in
nscaler, & ! in
ft, & ! in
bc_in(s)%t_veg_pa(ifp), & ! in
lmr_z(iv,ft,cl)) ! out
case (lmrmodel_ryan_1991)

call LeafLayerMaintenanceRespiration_Ryan_1991( lnc_top, & ! in
nscaler, & ! in
ft, & ! in
bc_in(s)%t_veg_pa(ifp), & ! in
lmr_z(iv,ft,cl)) ! out

case (lmrmodel_atkin_etal_2017)

call LeafLayerMaintenanceRespiration_Atkin_etal_2017(lnc_top, & ! in
nscaler, & ! in
ft, & ! in
bc_in(s)%t_veg_pa(ifp), & ! in
currentPatch%tveg_lpa%GetMean(), & ! in
lmr_z(iv,ft,cl)) ! out

case default

write (fates_log(),*)'error, incorrect leaf respiration model specified'
call endrun(msg=errMsg(sourcefile, __LINE__))

end select

! Part VII: Calculate (1) maximum rate of carboxylation (vcmax),
! (2) maximum electron transport rate, (3) triose phosphate
Expand Down Expand Up @@ -755,7 +767,7 @@ subroutine FatesPlantRespPhotosynthDrive (nsites, sites,bc_in,bc_out,dtime)
if ( int(woody(ft)) == itrue) then
tcwood = q10_mr**((bc_in(s)%t_veg_pa(ifp)-tfrz - 20.0_r8)/10.0_r8)
! kgC/s = kgN * kgC/kgN/s
currentCohort%livestem_mr = live_stem_n * ED_val_base_mr_20 * tcwood * maintresp_reduction_factor
currentCohort%livestem_mr = live_stem_n * maintresp_nonleaf_baserate * tcwood * maintresp_reduction_factor
else
currentCohort%livestem_mr = 0._r8
end if
Expand All @@ -774,7 +786,7 @@ subroutine FatesPlantRespPhotosynthDrive (nsites, sites,bc_in,bc_out,dtime)
do j = 1,bc_in(s)%nlevsoil
tcsoi = q10_mr**((bc_in(s)%t_soisno_sl(j)-tfrz - 20.0_r8)/10.0_r8)

fnrt_mr_layer = fnrt_n * ED_val_base_mr_20 * tcsoi * rootfr_ft(ft,j) * maintresp_reduction_factor
fnrt_mr_layer = fnrt_n * maintresp_nonleaf_baserate * tcsoi * rootfr_ft(ft,j) * maintresp_reduction_factor

! calculate the cost of carbon for N fixation in each soil layer and calculate N fixation rate based on that [kgC / kgN]

Expand All @@ -795,7 +807,7 @@ subroutine FatesPlantRespPhotosynthDrive (nsites, sites,bc_in,bc_out,dtime)
! Soil temperature used to adjust base rate of MR
tcsoi = q10_mr**((bc_in(s)%t_soisno_sl(j)-tfrz - 20.0_r8)/10.0_r8)
currentCohort%livecroot_mr = currentCohort%livecroot_mr + &
live_croot_n * ED_val_base_mr_20 * tcsoi * &
live_croot_n * maintresp_nonleaf_baserate * tcsoi * &
rootfr_ft(ft,j) * maintresp_reduction_factor
enddo
else
Expand Down Expand Up @@ -827,6 +839,9 @@ subroutine FatesPlantRespPhotosynthDrive (nsites, sites,bc_in,bc_out,dtime)

currentCohort%resp_m = currentCohort%resp_m + currentCohort%rdark

! save as a diagnostic the un-throttled maintenance respiration to be able to know how strong this is
currentCohort%resp_m_unreduced = currentCohort%resp_m / maintresp_reduction_factor

! convert from kgC/indiv/s to kgC/indiv/timestep
currentCohort%resp_m = currentCohort%resp_m * dtime
currentCohort%gpp_tstep = currentCohort%gpp_tstep * dtime
Expand Down Expand Up @@ -2046,22 +2061,35 @@ end subroutine GetCanopyGasParameters

! ====================================================================================

subroutine LeafLayerMaintenanceRespiration(lmr25top_ft, &
nscaler, &
ft, &
subroutine LeafLayerMaintenanceRespiration_Ryan_1991(lnc_top, &
nscaler, &
ft, &
veg_tempk, &
lmr)

use FatesConstantsMod, only : tfrz => t_water_freeze_k_1atm
use FatesConstantsMod, only : umolC_to_kgC
use FatesConstantsMod, only : g_per_kg
use EDPftvarcon , only : EDPftvarcon_inst

! -----------------------------------------------------------------------
! Base maintenance respiration rate for plant tissues maintresp_leaf_ryan1991_baserate
! M. Ryan, 1991. Effects of climate change on plant respiration.
! Ecological Applications, 1(2), 157-167.
! Original expression is br = 0.0106 molC/(molN h)
! Conversion by molecular weights of C and N gives 2.525e-6 gC/(gN s)
! Which is the default value of maintresp_nonleaf_baserate

! Arguments
real(r8), intent(in) :: lmr25top_ft ! canopy top leaf maint resp rate at 25C
! for this pft (umol CO2/m**2/s)
integer, intent(in) :: ft ! (plant) Functional Type Index
real(r8), intent(in) :: lnc_top ! Leaf nitrogen content per unit area at canopy top [gN/m2]
real(r8), intent(in) :: nscaler ! Scale for leaf nitrogen profile
integer, intent(in) :: ft ! (plant) Functional Type Index
real(r8), intent(in) :: veg_tempk ! vegetation temperature
real(r8), intent(out) :: lmr ! Leaf Maintenance Respiration (umol CO2/m**2/s)

! Locals
real(r8) :: lmr25 ! leaf layer: leaf maintenance respiration rate at 25C (umol CO2/m**2/s)
real(r8) :: lmr25top ! canopy top leaf maint resp rate at 25C for this pft (umol CO2/m**2/s)

! Parameter
real(r8), parameter :: lmrha = 46390._r8 ! activation energy for lmr (J/mol)
Expand All @@ -2070,26 +2098,84 @@ subroutine LeafLayerMaintenanceRespiration(lmr25top_ft, &
real(r8), parameter :: lmrc = 1.15912391_r8 ! scaling factor for high
! temperature inhibition (25 C = 1.0)



lmr25top = EDPftvarcon_inst%maintresp_leaf_ryan1991_baserate(ft) * (1.5_r8 ** ((25._r8 - 20._r8)/10._r8))
lmr25top = lmr25top * lnc_top / (umolC_to_kgC * g_per_kg)


! Part I: Leaf Maintenance respiration: umol CO2 / m**2 [leaf] / s
! ----------------------------------------------------------------------------------
lmr25 = lmr25top_ft * nscaler
lmr25 = lmr25top * nscaler

if ( nint(EDpftvarcon_inst%c3psn(ft)) == 1)then
if (nint(EDPftvarcon_inst%c3psn(ft)) /= 1) then
! temperature sensitivity of C3 plants
lmr = lmr25 * ft1_f(veg_tempk, lmrha) * &
fth_f(veg_tempk, lmrhd, lmrse, lmrc)
fth_f(veg_tempk, lmrhd, lmrse, lmrc)
else
! temperature sensitivity of C4 plants
lmr = lmr25 * 2._r8**((veg_tempk-(tfrz+25._r8))/10._r8)
lmr = lmr / (1._r8 + exp( 1.3_r8*(veg_tempk-(tfrz+55._r8)) ))
end if
endif

! Any hydrodynamic limitations could go here, currently none
! lmr = lmr * (nothing)

end subroutine LeafLayerMaintenanceRespiration
end subroutine LeafLayerMaintenanceRespiration_Ryan_1991

! ====================================================================================

subroutine LeafLayerMaintenanceRespiration_Atkin_etal_2017(lnc_top, &
nscaler, &
ft, &
veg_tempk, &
tgrowth, &
lmr)

use FatesConstantsMod, only : tfrz => t_water_freeze_k_1atm
use FatesConstantsMod, only : umolC_to_kgC
use FatesConstantsMod, only : g_per_kg
use EDPftvarcon , only : EDPftvarcon_inst

! Arguments
real(r8), intent(in) :: lnc_top ! Leaf nitrogen content per unit area at canopy top [gN/m2]
integer, intent(in) :: ft ! (plant) Functional Type Index
real(r8), intent(in) :: nscaler ! Scale for leaf nitrogen profile
real(r8), intent(in) :: veg_tempk ! vegetation temperature (degrees K)
real(r8), intent(in) :: tgrowth ! lagged vegetation temperature averaged over acclimation timescale (degrees K)
real(r8), intent(out) :: lmr ! Leaf Maintenance Respiration (umol CO2/m**2/s)

! Locals
real(r8) :: lmr25 ! leaf layer: leaf maintenance respiration rate at 25C (umol CO2/m**2/s)
real(r8) :: r_0 ! base respiration rate, PFT-dependent (umol CO2/m**2/s)
real(r8) :: r_t_ref ! acclimated ref respiration rate (umol CO2/m**2/s)
real(r8) :: lmr25top ! canopy top leaf maint resp rate at 25C for this pft (umol CO2/m**2/s)

! Parameters
! values from Atkin et al., 2017 https://doi.org/10.1007/978-3-319-68703-2_6
! and Heskel et al., 2016 https://doi.org/10.1073/pnas.1520282113
real(r8), parameter :: b = 0.1012_r8 ! (degrees C**-1)
real(r8), parameter :: c = -0.0005_r8 ! (degrees C**-2)
real(r8), parameter :: TrefC = 25._r8 ! (degrees C)
real(r8), parameter :: r_1 = 0.2061_r8 ! (umol CO2/m**2/s / (gN/(m2 leaf)))
real(r8), parameter :: r_2 = -0.0402_r8 ! (umol CO2/m**2/s/degree C)

! parameter values of r_0 as listed in Atkin et al 2017: (umol CO2/m**2/s)
! Broad-leaved trees 1.7560
! Needle-leaf trees 1.4995
! Shrubs 2.0749
! C3 herbs/grasses 2.1956
! In the absence of better information, we use the same value for C4 grasses as C3 grasses.

! note that this code uses the relationship between leaf N and respiration from Atkin et al
! for the top of the canopy, but then assumes proportionality with N through the canopy.

! r_0 currently put into the EDPftvarcon_inst%dev_arbitrary_pft
! all figs in Atkin et al 2017 stop at zero Celsius so we will assume acclimation is fixed below that
r_0 = EDPftvarcon_inst%maintresp_leaf_atkin2017_baserate(ft)
r_t_ref = nscaler * (r_0 + r_1 * lnc_top + r_2 * max(0._r8, (tgrowth - tfrz) ))

lmr = r_t_ref * exp(b * (veg_tempk - tfrz - TrefC) + c * ((veg_tempk-tfrz)**2 - TrefC**2))

end subroutine LeafLayerMaintenanceRespiration_Atkin_etal_2017

! ====================================================================================

Expand Down
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